Files
clawhdf5/crates/clawhdf5-format/src/fractal_heap.rs
T
osobhandClaude Opus 5.5 42894bf93b format: v2 B-trees, dense groups and group listings over Storage
BTreeV2Header::parse_in, collect_btree_v2_records_in and
find_btree_v2_records_in read one bounded window per node (its size is
known from the parent before the node is read; a count stretched past
node_size is checked against the end of the file first), with the
whole-file bounds errors unchanged. With them, dense attributes, a SOHM
B-tree index and huge fractal-heap objects no longer answer
ContiguousStorageRequired, and group_v1/group_v2 listings, lookups and
path resolution get *_in cores (resolve_group_children_in,
resolve_child_in, resolve_path_any_in, ...). The &[u8] functions are
thin wrappers, as in M1.

The equivalence harness now fails on any ContiguousStorageRequired and
compares v2 B-tree headers, records and descents, group listings, child
lookups and paths; a unit test compares a two-level tree through a
read_at-only storage truncated at every length and with every node byte
flipped.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-26 16:13:01 -05:00

1362 lines
52 KiB
Rust

//! HDF5 Fractal Heap parsing for v2 group link storage.
#[cfg(not(feature = "std"))]
use alloc::{format, vec::Vec};
#[cfg(feature = "checksum")]
use byteorder::{ByteOrder, LittleEndian};
use crate::addr::to_usize;
use crate::btree_v2::{BTreeV2Header, find_btree_v2_records_in};
use crate::error::FormatError;
use crate::filter_pipeline::FilterPipeline;
use crate::storage::{Storage, Window, len_usize, read_exact_at};
/// Parsed fractal heap header (signature "FRHP").
#[derive(Debug, Clone)]
pub struct FractalHeapHeader {
/// Length of heap IDs in bytes (typically 7).
pub heap_id_length: u16,
/// I/O filter encoded length (0 = no filters).
pub io_filter_encoded_length: u16,
/// Maximum size of a managed object.
pub max_managed_object_size: u32,
/// Width of the doubling table.
pub table_width: u16,
/// Starting block size in the doubling table.
pub starting_block_size: u64,
/// Maximum direct block size.
pub max_direct_block_size: u64,
/// Maximum heap size in bits (determines offset bit width in heap IDs).
pub max_heap_size: u16,
/// Starting row of indirect blocks in the doubling table.
pub starting_row_of_indirect_blocks: u16,
/// Address of the root block.
pub root_block_address: u64,
/// Number of rows in root indirect block (0 = root is direct block).
pub current_rows_in_root_indirect_block: u16,
/// Total number of managed objects.
pub managed_objects_count: u64,
/// Address of the v2 B-tree indexing "huge" objects (undefined address
/// when the heap has none). Huge objects are those larger than
/// `max_managed_object_size`; they live outside the heap's blocks.
pub huge_btree_address: u64,
/// The heap's I/O filter pipeline, if it has one. It applies to managed
/// direct blocks and to huge objects.
pub filter_pipeline: Option<FilterPipeline>,
/// Stored (filtered) size of the root direct block; meaningful only when
/// the heap is filtered and its root is a direct block.
pub root_direct_block_filtered_size: u64,
/// Filter mask of the root direct block (bit *i* set = filter *i*
/// skipped); meaningful only when the heap is filtered.
pub root_direct_block_filter_mask: u32,
/// Size of addresses in the file ("Size of Offsets").
pub offset_size: u8,
/// Size of lengths in the file ("Size of Lengths").
pub length_size: u8,
}
fn read_offset(data: &[u8], pos: usize, size: u8) -> Result<u64, FormatError> {
let s = size as usize;
if pos.checked_add(s).is_none_or(|end| end > data.len()) {
return Err(FormatError::UnexpectedEof {
expected: pos.saturating_add(s),
available: data.len(),
});
}
Ok(match size {
2 => u16::from_le_bytes([data[pos], data[pos + 1]]) as u64,
4 => u32::from_le_bytes([data[pos], data[pos + 1], data[pos + 2], data[pos + 3]]) as u64,
8 => u64::from_le_bytes([
data[pos],
data[pos + 1],
data[pos + 2],
data[pos + 3],
data[pos + 4],
data[pos + 5],
data[pos + 6],
data[pos + 7],
]),
_ => return Err(FormatError::InvalidOffsetSize(size)),
})
}
fn ensure_len(data: &[u8], pos: usize, needed: usize) -> Result<(), FormatError> {
match pos.checked_add(needed) {
Some(end) if end <= data.len() => Ok(()),
_ => Err(FormatError::UnexpectedEof {
expected: pos.saturating_add(needed),
available: data.len(),
}),
}
}
fn is_undefined(val: u64, offset_size: u8) -> bool {
match offset_size {
2 => val == 0xFFFF,
4 => val == 0xFFFF_FFFF,
8 => val == 0xFFFF_FFFF_FFFF_FFFF,
_ => false,
}
}
/// Little-endian unsigned integer of up to 8 bytes.
fn le_uint(bytes: &[u8]) -> u64 {
bytes
.iter()
.take(8)
.enumerate()
.fold(0u64, |acc, (i, &b)| acc | (u64::from(b) << (i * 8)))
}
fn heap_error(msg: &str) -> FormatError {
FormatError::ChunkedReadError(format!("fractal heap: {msg}"))
}
/// Heap ID type, from bits 4-5 of an ID's first byte (libhdf5's
/// `H5HF_ID_TYPE_MASK`, 0x30); bits 6-7 are the ID version, which must be 0.
const HEAP_ID_MANAGED: u8 = 0;
const HEAP_ID_HUGE: u8 = 1;
const HEAP_ID_TINY: u8 = 2;
/// The type (0 managed, 1 huge, 2 tiny) of a heap ID from its first byte,
/// refusing an ID version other than 0.
fn heap_id_type(first: u8) -> Result<u8, FormatError> {
if first >> 6 != 0 {
return Err(heap_error("unsupported heap ID version"));
}
Ok((first >> 4) & 0x03)
}
/// v2 B-tree record types indexing a heap's huge objects.
const BTREE_HUGE_INDIRECT: u8 = 1;
const BTREE_HUGE_INDIRECT_FILTERED: u8 = 2;
impl FractalHeapHeader {
/// Parse a fractal heap header at the given offset.
pub fn parse(
file_data: &[u8],
offset: usize,
offset_size: u8,
length_size: u8,
) -> Result<FractalHeapHeader, FormatError> {
Self::parse_in(file_data, offset as u64, offset_size, length_size)
}
/// [`Self::parse`] over any [`Storage`]: one read of the header (two
/// when it holds an I/O filter pipeline).
pub fn parse_in<S: Storage + ?Sized>(
file: &S,
offset: u64,
offset_size: u8,
length_size: u8,
) -> Result<FractalHeapHeader, FormatError> {
// Every field up to the checksum, without and with the filter
// information; the window holds all of it (or ends at the end of
// the file), so its bounds checks are the whole-file ones.
let (os, ls) = (usize::from(offset_size), usize::from(length_size));
let unfiltered_len = 26 + 12 * ls + 3 * os;
let mut w = Window::read(file, offset, unfiltered_len)?;
if w.bytes.len() == unfiltered_len {
let filter_len = usize::from(u16::from_le_bytes([w.bytes[7], w.bytes[8]]));
if filter_len > 0 {
w = Window::read(file, offset, unfiltered_len + ls + 4 + filter_len)?;
}
}
let ensure_len = |_: &[u8], pos: usize, needed: usize| w.ensure(pos, needed);
let read_offset = |_: &[u8], pos: usize, size: u8| {
w.ensure(pos, usize::from(size))?;
read_offset(&w.bytes, pos, size)
};
let file_data: &[u8] = &w.bytes;
let offset = 0usize;
ensure_len(file_data, offset, 5)?;
if &file_data[offset..offset + 4] != b"FRHP" {
return Err(FormatError::InvalidFractalHeapSignature);
}
let version = file_data[offset + 4];
if version != 0 {
return Err(FormatError::InvalidFractalHeapVersion(version));
}
let mut pos = offset + 5;
ensure_len(file_data, pos, 2)?;
let heap_id_length = u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
ensure_len(file_data, pos, 2)?;
let io_filter_encoded_length = u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
ensure_len(file_data, pos, 1)?;
let _flags = file_data[pos];
pos += 1;
ensure_len(file_data, pos, 4)?;
let max_managed_object_size = u32::from_le_bytes([
file_data[pos],
file_data[pos + 1],
file_data[pos + 2],
file_data[pos + 3],
]);
pos += 4;
// next_huge_object_id (length_size)
ensure_len(file_data, pos, ls)?;
pos += ls;
// btree_huge_objects_address (offset_size)
let huge_btree_address = read_offset(file_data, pos, offset_size)?;
pos += os;
// Skip: free_space_managed_blocks(ls), managed_block_free_space_manager_address(os),
// managed_space_in_heap(ls), allocated_managed_space_in_heap(ls),
// direct_block_allocation_iterator_offset(ls)
let skip_size = 4 * ls + os;
ensure_len(file_data, pos, skip_size)?;
pos += skip_size;
// managed_objects_count (length_size)
let managed_objects_count = read_offset(file_data, pos, length_size)?;
pos += ls;
// huge_objects_size, huge_objects_count, tiny_objects_size,
// tiny_objects_count (length_size each)
pos += 4 * ls;
// table_width (2)
ensure_len(file_data, pos, 2)?;
let table_width = u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
// starting_block_size (length_size)
let starting_block_size = read_offset(file_data, pos, length_size)?;
pos += ls;
// max_direct_block_size (length_size)
let max_direct_block_size = read_offset(file_data, pos, length_size)?;
pos += ls;
// max_heap_size (2)
ensure_len(file_data, pos, 2)?;
let max_heap_size = u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
// starting_row_of_indirect_blocks (2)
ensure_len(file_data, pos, 2)?;
let starting_row_of_indirect_blocks =
u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
// root_block_address (offset_size)
let root_block_address = read_offset(file_data, pos, offset_size)?;
pos += os;
// current_rows_in_root_indirect_block (2)
ensure_len(file_data, pos, 2)?;
let current_rows_in_root_indirect_block =
u16::from_le_bytes([file_data[pos], file_data[pos + 1]]);
pos += 2;
// With I/O filters: root direct block's filtered size (length_size),
// its filter mask (4), then the encoded filter pipeline message.
let mut filter_pipeline = None;
let mut root_direct_block_filtered_size = 0;
let mut root_direct_block_filter_mask = 0;
if io_filter_encoded_length > 0 {
root_direct_block_filtered_size = read_offset(file_data, pos, length_size)?;
pos += ls;
ensure_len(file_data, pos, 4)?;
root_direct_block_filter_mask = u32::from_le_bytes([
file_data[pos],
file_data[pos + 1],
file_data[pos + 2],
file_data[pos + 3],
]);
pos += 4;
let n = io_filter_encoded_length as usize;
ensure_len(file_data, pos, n)?;
filter_pipeline = Some(FilterPipeline::parse(&file_data[pos..pos + n])?);
pos += n;
}
// Validate header checksum
#[cfg(feature = "checksum")]
{
ensure_len(file_data, pos, 4)?;
let stored = LittleEndian::read_u32(&file_data[pos..pos + 4]);
let computed = crate::checksum::jenkins_lookup3(&file_data[offset..pos]);
if computed != stored {
return Err(FormatError::ChecksumMismatch {
expected: stored,
computed,
});
}
}
#[cfg(not(feature = "checksum"))]
let _ = pos;
Ok(FractalHeapHeader {
heap_id_length,
io_filter_encoded_length,
max_managed_object_size,
table_width,
starting_block_size,
max_direct_block_size,
max_heap_size,
starting_row_of_indirect_blocks,
root_block_address,
current_rows_in_root_indirect_block,
managed_objects_count,
huge_btree_address,
filter_pipeline,
root_direct_block_filtered_size,
root_direct_block_filter_mask,
offset_size,
length_size,
})
}
/// Decode a managed heap ID into (offset_in_heap, object_length).
///
/// The heap ID layout for managed objects (type 0):
/// - Byte 0: bits 6-7 = version (0), bits 4-5 = type (0), bits 0-3 = reserved
/// - Bytes 1+: offset (max_heap_size bits, LE) then length (remaining bits, LE)
pub fn decode_managed_id(&self, id_bytes: &[u8]) -> Result<(u64, u64), FormatError> {
if id_bytes.is_empty() {
return Err(FormatError::UnexpectedEof {
expected: 1,
available: 0,
});
}
let id_type = heap_id_type(id_bytes[0])?;
if id_type != HEAP_ID_MANAGED {
return Err(FormatError::InvalidHeapIdType(id_type));
}
// Bytes 1+ contain offset and length packed in little-endian order.
// offset uses max_heap_size bits, length uses the remaining bits.
let payload = &id_bytes[1..];
let mut combined: u64 = 0;
for (i, &b) in payload.iter().enumerate() {
if i >= 8 {
break;
}
combined |= (b as u64) << (i * 8);
}
let offset_bits = self.max_heap_size as u32;
let offset_mask = if offset_bits >= 64 {
u64::MAX
} else {
(1u64 << offset_bits) - 1
};
let heap_offset = combined & offset_mask;
let total_payload_bits = (payload.len() as u32) * 8;
let length_bits = total_payload_bits.saturating_sub(offset_bits);
let length_val = if length_bits == 0 {
0
} else {
let length_mask = if length_bits >= 64 {
u64::MAX
} else {
(1u64 << length_bits) - 1
};
(combined >> offset_bits) & length_mask
};
Ok((heap_offset, length_val))
}
/// Read any object from the heap given its raw heap ID bytes: managed
/// (stored in the heap's blocks), huge (stored outside them, found
/// directly from the ID or through the huge-object v2 B-tree, optionally
/// filtered) or tiny (stored in the ID itself).
///
/// Despite its name this accepts every ID type; `offset_size` must match
/// the one the header was parsed with.
pub fn read_managed_object(
&self,
file_data: &[u8],
id_bytes: &[u8],
offset_size: u8,
) -> Result<Vec<u8>, FormatError> {
self.read_managed_object_in(file_data, id_bytes, offset_size)
}
/// [`Self::read_managed_object`] over any [`Storage`].
pub fn read_managed_object_in<S: Storage + ?Sized>(
&self,
file_data: &S,
id_bytes: &[u8],
offset_size: u8,
) -> Result<Vec<u8>, FormatError> {
crate::lookup_stats::heap_object_read();
let Some(&first) = id_bytes.first() else {
return Err(FormatError::UnexpectedEof {
expected: 1,
available: 0,
});
};
match heap_id_type(first)? {
HEAP_ID_MANAGED => self.read_heap_managed(file_data, id_bytes, offset_size),
HEAP_ID_HUGE => self.read_huge_object(file_data, id_bytes),
HEAP_ID_TINY => self.read_tiny_object(id_bytes),
other => Err(FormatError::InvalidHeapIdType(other)),
}
}
/// Whether a huge object's ID holds its address and length directly
/// (libhdf5 does this when they fit in the ID), rather than a key into
/// the huge-object B-tree.
fn huge_ids_direct(&self) -> bool {
let room = usize::from(self.heap_id_length).saturating_sub(1);
let os = usize::from(self.offset_size);
let ls = usize::from(self.length_size);
if self.filter_pipeline.is_some() {
room >= os + ls + 4 + ls
} else {
room >= os + ls
}
}
/// Read a huge object (heap ID type 1).
fn read_huge_object<S: Storage + ?Sized>(
&self,
file: &S,
id: &[u8],
) -> Result<Vec<u8>, FormatError> {
let os = usize::from(self.offset_size);
let ls = usize::from(self.length_size);
// (address, stored length, filter mask, decoded length); the last two
// only matter for a filtered heap.
let (addr, stored_len, mask, mem_len) = if self.huge_ids_direct() {
let body = &id[1..];
let need = if self.filter_pipeline.is_some() {
os + ls + 4 + ls
} else {
os + ls
};
ensure_len(body, 0, need)?;
let addr = le_uint(&body[..os]);
let len = le_uint(&body[os..os + ls]);
if self.filter_pipeline.is_some() {
let mask = u32::from_le_bytes([
body[os + ls],
body[os + ls + 1],
body[os + ls + 2],
body[os + ls + 3],
]);
let mem = le_uint(&body[os + ls + 4..os + ls + 4 + ls]);
(addr, len, mask, mem)
} else {
(addr, len, 0, len)
}
} else {
let key_len = (usize::from(self.heap_id_length).saturating_sub(1)).min(8);
ensure_len(id, 1, key_len)?;
let key = le_uint(&id[1..1 + key_len]);
self.find_huge_record(file, key)?
};
let start = usize::try_from(addr).map_err(|_| heap_error("huge object address"))?;
let len = usize::try_from(stored_len).map_err(|_| heap_error("huge object length"))?;
let stored = read_exact_at(file, start as u64, len)?;
match &self.filter_pipeline {
None => Ok(stored.into_owned()),
Some(pipeline) => {
let mem = usize::try_from(mem_len).map_err(|_| heap_error("huge object size"))?;
let out = crate::filters::decompress_chunk_masked(&stored, pipeline, mem, 1, mask)?;
if out.len() != mem {
return Err(heap_error("filtered huge object decoded to the wrong size"));
}
Ok(out)
}
}
}
/// Look up huge object `key` in the huge-object v2 B-tree, returning
/// (address, stored length, filter mask, decoded length).
fn find_huge_record<S: Storage + ?Sized>(
&self,
file: &S,
key: u64,
) -> Result<(u64, u64, u32, u64), FormatError> {
if is_undefined(self.huge_btree_address, self.offset_size) {
return Err(heap_error(
"huge object ID but the heap has no huge-object index",
));
}
let hdr = BTreeV2Header::parse_in(
file,
self.huge_btree_address,
self.offset_size,
self.length_size,
)?;
let os = usize::from(self.offset_size);
let ls = usize::from(self.length_size);
let filtered = self.filter_pipeline.is_some();
let (expected_type, rec_len) = if filtered {
(BTREE_HUGE_INDIRECT_FILTERED, os + ls + 4 + ls + ls)
} else {
(BTREE_HUGE_INDIRECT, os + ls + ls)
};
if hdr.tree_type != expected_type || usize::from(hdr.record_size) < rec_len {
return Err(heap_error("unexpected huge-object B-tree record type"));
}
// Records are ordered by ID (the last field): descend to the ones
// equal to `key` instead of reading the whole index.
let id_at = rec_len - ls;
let records = find_btree_v2_records_in(file, &hdr, self.offset_size, &mut |r| {
le_uint(&r[id_at..id_at + ls]).cmp(&key)
})?;
for rec in &records {
let d = &rec.data;
if d.len() < rec_len {
continue;
}
let addr = le_uint(&d[..os]);
let len = le_uint(&d[os..os + ls]);
if filtered {
let mask = u32::from_le_bytes([
d[os + ls],
d[os + ls + 1],
d[os + ls + 2],
d[os + ls + 3],
]);
let mem = le_uint(&d[os + ls + 4..os + 2 * ls + 4]);
let id = le_uint(&d[os + 2 * ls + 4..os + 3 * ls + 4]);
if id == key {
return Ok((addr, len, mask, mem));
}
} else {
let id = le_uint(&d[os + ls..os + 2 * ls]);
if id == key {
return Ok((addr, len, 0, len));
}
}
}
Err(heap_error("huge object not found in its B-tree"))
}
/// Read a tiny object (heap ID type 2), stored in the ID itself.
fn read_tiny_object(&self, id: &[u8]) -> Result<Vec<u8>, FormatError> {
// libhdf5 uses a one-byte length (low 4 bits of byte 0) unless the ID
// is long enough to need 12 bits, which then borrow byte 1.
let extended = usize::from(self.heap_id_length).saturating_sub(1) > 17;
let (len, start) = if extended {
ensure_len(id, 0, 2)?;
(
((usize::from(id[0] & 0x0F)) << 8 | usize::from(id[1])) + 1,
2,
)
} else {
(usize::from(id[0] & 0x0F) + 1, 1)
};
ensure_len(id, start, len)?;
Ok(id[start..start + len].to_vec())
}
/// Read a managed object (heap ID type 0).
fn read_heap_managed<S: Storage + ?Sized>(
&self,
file_data: &S,
id_bytes: &[u8],
offset_size: u8,
) -> Result<Vec<u8>, FormatError> {
let (heap_offset, obj_len) = self.decode_managed_id(id_bytes)?;
if is_undefined(self.root_block_address, offset_size) {
return Err(FormatError::UnexpectedEof {
expected: 1,
available: 0,
});
}
if self.current_rows_in_root_indirect_block == 0 {
// Root is a direct block
self.read_from_direct_block(
file_data,
DirectBlock {
addr: to_usize(self.root_block_address)?,
size: self.starting_block_size,
heap_offset: 0,
filtered_size: self.root_direct_block_filtered_size,
filter_mask: self.root_direct_block_filter_mask,
},
heap_offset,
to_usize(obj_len)?,
)
} else {
// Root is an indirect block — limit recursion to 64 levels
self.read_from_indirect_block(
file_data,
to_usize(self.root_block_address)?,
self.current_rows_in_root_indirect_block,
0, // block offset
heap_offset,
to_usize(obj_len)?,
offset_size,
64, // max recursion depth
)
}
}
/// Read an object from a direct block.
///
/// The heap offset is relative to the start of the block (including its
/// header), so we just add it to the block address minus the block's heap
/// offset. A filtered heap stores each direct block (header included)
/// through its filter pipeline, so the block is decoded first.
fn read_from_direct_block<S: Storage + ?Sized>(
&self,
file: &S,
block: DirectBlock,
target_offset: u64,
length: usize,
) -> Result<Vec<u8>, FormatError> {
if target_offset < block.heap_offset {
return Err(FormatError::UnexpectedEof {
expected: to_usize(block.heap_offset)?,
available: to_usize(target_offset)?,
});
}
let local_offset = to_usize(target_offset - block.heap_offset)?;
if let Some(pipeline) = &self.filter_pipeline {
let stored_len = usize::try_from(block.filtered_size)
.map_err(|_| heap_error("direct block size"))?;
let size = usize::try_from(block.size).map_err(|_| heap_error("direct block size"))?;
let stored = read_exact_at(file, block.addr as u64, stored_len)?;
let decoded = crate::filters::decompress_chunk_masked(
&stored,
pipeline,
size,
1,
block.filter_mask,
)?;
ensure_len(&decoded, local_offset, length)?;
return Ok(decoded[local_offset..local_offset + length].to_vec());
}
let pos = block
.addr
.checked_add(local_offset)
.ok_or(FormatError::UnexpectedEof {
expected: usize::MAX,
available: len_usize(file),
})?;
Ok(read_exact_at(file, pos as u64, length)?.into_owned())
}
/// Read an object by traversing an indirect block to find the right direct block.
#[allow(clippy::too_many_arguments)]
fn read_from_indirect_block<S: Storage + ?Sized>(
&self,
file: &S,
iblock_addr: usize,
nrows: u16,
iblock_heap_offset: u64,
target_offset: u64,
length: usize,
offset_size: u8,
depth_remaining: u16,
) -> Result<Vec<u8>, FormatError> {
if depth_remaining == 0 {
return Err(FormatError::ChunkedReadError(
"fractal heap: maximum recursion depth exceeded".into(),
));
}
let block_offset_bytes = (self.max_heap_size as usize).div_ceil(8);
let iblock_header = 5 + offset_size as usize + block_offset_bytes;
let nrows_usize = nrows as usize;
// Rows below max_direct_rows hold direct blocks; rows at/above hold
// child indirect blocks. (NOT the FRHP "starting rows" field.)
let start_indirect = self.max_direct_rows();
let max_direct_rows = nrows_usize.min(start_indirect);
// The block up to its last child entry. The walk below reads
// entries in order and stops at the one covering the target, which
// the geometry alone locates, so the first window ends there: a
// header claiming a huge table costs a read of the entries in front
// of the target, not of the rest of the file. Only when that entry
// is unallocated (or none covers the target) does the walk go on,
// over the whole block. Either window holds what it was asked for or
// ends at the end of the file, so its bounds checks are the
// whole-file ones.
let direct_entry = usize::from(offset_size)
+ if self.filter_pipeline.is_some() {
usize::from(self.length_size) + 4
} else {
0
};
let direct_entries = max_direct_rows.saturating_mul(usize::from(self.table_width));
let entries_len = |n: usize| {
n.min(direct_entries)
.saturating_mul(direct_entry)
.saturating_add(
n.saturating_sub(direct_entries)
.saturating_mul(usize::from(offset_size)),
)
};
let all_entries = direct_entries.saturating_add(
nrows_usize
.saturating_sub(start_indirect)
.saturating_mul(usize::from(self.table_width)),
);
let block_len = iblock_header.saturating_add(entries_len(all_entries));
let target_entry = self.indirect_entry_for(nrows_usize, iblock_heap_offset, target_offset);
let first_len = target_entry.map_or(block_len, |i| {
iblock_header
.saturating_add(entries_len(i.saturating_add(1)))
.min(block_len)
});
let mut next = self.walk_indirect_block(
&Window::read(file, iblock_addr as u64, first_len)?,
nrows_usize,
iblock_heap_offset,
target_offset,
offset_size,
target_entry.map_or(usize::MAX, |i| i.saturating_add(1)),
)?;
if next.is_none() && first_len < block_len {
next = self.walk_indirect_block(
&Window::read(file, iblock_addr as u64, block_len)?,
nrows_usize,
iblock_heap_offset,
target_offset,
offset_size,
usize::MAX,
)?;
}
match next {
Some(IndirectChild::Direct(block)) => {
self.read_from_direct_block(file, block, target_offset, length)
}
Some(IndirectChild::Indirect {
addr,
nrows,
heap_offset,
}) => self.read_from_indirect_block(
file,
addr,
nrows,
heap_offset,
target_offset,
length,
offset_size,
depth_remaining - 1,
),
None => Err(FormatError::UnexpectedEof {
expected: to_usize(target_offset)?.saturating_add(length),
available: len_usize(file),
}),
}
}
/// Which child entry of an indirect block (numbered in walk order:
/// direct rows, then indirect rows) covers `target_offset`, from the
/// doubling-table geometry alone — the entry
/// [`Self::walk_indirect_block`] stops at if it is allocated. `None`
/// when no entry does.
fn indirect_entry_for(&self, nrows: usize, heap_offset: u64, target: u64) -> Option<usize> {
// The walk adds block sizes with saturation; in u128 the same test
// is `cur <= target < cur + size` without it (a target of u64::MAX
// is never inside a saturated range).
if target == u64::MAX {
return None;
}
let (tw, target) = (u128::from(self.table_width), u128::from(target));
let mut cur = u128::from(heap_offset);
let mut before = 0usize;
for row in 0..nrows {
if target < cur {
return None;
}
// Direct and indirect rows alike span this row's block size per
// entry.
let size = u128::from(self.block_size_for_row(row));
let span = size * tw;
if size > 0 && target < cur + span {
let col = usize::try_from((target - cur) / size).ok()?;
return before.checked_add(col);
}
cur += span;
before = before.saturating_add(self.table_width as usize);
}
None
}
/// Walk an indirect block's child entries in order, in the window `w`
/// (the block from its signature on), and return the allocated child
/// covering `target_offset`, or `None` when no entry among the first
/// `limit` does.
fn walk_indirect_block(
&self,
w: &Window<'_>,
nrows: usize,
iblock_heap_offset: u64,
target_offset: u64,
offset_size: u8,
limit: usize,
) -> Result<Option<IndirectChild>, FormatError> {
let ensure_len = |_: &[u8], pos: usize, needed: usize| w.ensure(pos, needed);
let read_offset = |_: &[u8], pos: usize, size: u8| {
w.ensure(pos, usize::from(size))?;
read_offset(&w.bytes, pos, size)
};
let file_data: &[u8] = &w.bytes;
let block_offset_bytes = (self.max_heap_size as usize).div_ceil(8);
let iblock_header = 5 + offset_size as usize + block_offset_bytes;
let tw = self.table_width as u64;
let mut current_heap_offset = iblock_heap_offset;
let start_indirect = self.max_direct_rows();
let max_direct_rows = nrows.min(start_indirect);
let mut walked = 0usize;
// Parse indirect block header
ensure_len(file_data, 0, 4)?;
if &file_data[..4] != b"FHIB" {
return Err(FormatError::InvalidFractalHeapSignature);
}
let mut pos = iblock_header;
for row in 0..max_direct_rows {
let block_size = self.block_size_for_row(row);
for _col in 0..tw {
if walked == limit {
return Ok(None);
}
walked += 1;
let child_addr = read_offset(file_data, pos, offset_size)?;
pos += offset_size as usize;
// A filtered heap stores each direct block's filtered size
// (length_size) and filter mask (4) after its address.
let (filtered_size, filter_mask) = if self.filter_pipeline.is_some() {
let size = read_offset(file_data, pos, self.length_size)?;
pos += usize::from(self.length_size);
ensure_len(file_data, pos, 4)?;
let mask = u32::from_le_bytes([
file_data[pos],
file_data[pos + 1],
file_data[pos + 2],
file_data[pos + 3],
]);
pos += 4;
(size, mask)
} else {
(0, 0)
};
let block_end = current_heap_offset.saturating_add(block_size);
if !is_undefined(child_addr, offset_size)
&& target_offset >= current_heap_offset
&& target_offset < block_end
{
return Ok(Some(IndirectChild::Direct(DirectBlock {
addr: to_usize(child_addr)?,
size: block_size,
heap_offset: current_heap_offset,
filtered_size,
filter_mask,
})));
}
current_heap_offset = block_end;
}
}
// Rows at and above `start_indirect` hold child indirect blocks. A
// child in row r spans exactly that row's block size of heap space,
// so it has as many rows as a table of that total size needs.
for row in start_indirect..nrows {
let child_space = self.block_size_for_row(row);
let child_nrows = self.rows_for_size(child_space);
for _col in 0..tw {
if walked == limit {
return Ok(None);
}
walked += 1;
let child_addr = read_offset(file_data, pos, offset_size)?;
pos += offset_size as usize;
let block_end = current_heap_offset.saturating_add(child_space);
if !is_undefined(child_addr, offset_size)
&& target_offset >= current_heap_offset
&& target_offset < block_end
{
return Ok(Some(IndirectChild::Indirect {
addr: to_usize(child_addr)?,
nrows: child_nrows,
heap_offset: current_heap_offset,
}));
}
current_heap_offset = block_end;
}
}
Ok(None)
}
/// Number of rows in the doubling table whose block size is at most the
/// maximum *direct* block size. Rows below this hold direct blocks; rows at
/// or above it hold child indirect blocks.
///
/// This is derived from the heap geometry, NOT the FRHP
/// "Starting # of Rows in Root Indirect Block" field (a constant, often 1)
/// — confusing the two makes a multi-direct-block heap unreadable.
fn max_direct_rows(&self) -> usize {
if self.starting_block_size == 0 {
return usize::MAX;
}
// Rows 0 and 1 share the starting block size; row r (r >= 1) is
// starting_block_size * 2^(r-1). The largest direct row reaches
// max_direct_block_size, giving log2(max/start) + 2 direct rows.
let ratio = (self.max_direct_block_size / self.starting_block_size).max(1);
let log2 = 63 - ratio.leading_zeros() as usize;
log2 + 2
}
/// Rows an indirect block needs to span `size` bytes of heap space:
/// `log2(size) - log2(starting_block_size * table_width) + 1`, as
/// libhdf5's `H5HF__dtable_size_to_rows`.
fn rows_for_size(&self, size: u64) -> u16 {
let log2 = |v: u64| 63u32.saturating_sub(v.max(1).leading_zeros());
let first_row_bits = log2(self.starting_block_size) + log2(u64::from(self.table_width));
(log2(size).saturating_sub(first_row_bits) + 1) as u16
}
/// Get block size for a given row in the doubling table.
fn block_size_for_row(&self, row: usize) -> u64 {
let sbs = self.starting_block_size;
if row <= 1 {
sbs
} else {
sbs.saturating_mul(1u64.checked_shl((row - 1) as u32).unwrap_or(u64::MAX))
}
}
}
/// A managed direct block's location, extent and (for a filtered heap) its
/// stored size and filter mask.
/// The child of an indirect block that covers a heap offset.
enum IndirectChild {
Direct(DirectBlock),
Indirect {
addr: usize,
nrows: u16,
heap_offset: u64,
},
}
struct DirectBlock {
addr: usize,
size: u64,
heap_offset: u64,
filtered_size: u64,
filter_mask: u32,
}
#[cfg(test)]
mod tests {
use super::*;
/// Build a minimal fractal heap with a single direct block at the root.
/// Returns (file_data, FractalHeapHeader) where file_data contains
/// the heap header at offset 0 and a direct block with known data.
fn build_simple_heap(offset_size: u8, length_size: u8) -> (Vec<u8>, usize) {
let os = offset_size as usize;
let ls = length_size as usize;
let max_heap_size: u16 = 16; // bits
let block_offset_bytes = (max_heap_size as usize).div_ceil(8); // 2
// Direct block at a known offset
let dblock_offset = 256usize;
let block_size: u64 = 128;
// Build fractal heap header at offset 0
let mut buf = vec![0u8; 1024];
let mut pos = 0;
buf[pos..pos + 4].copy_from_slice(b"FRHP");
pos += 4;
buf[pos] = 0; // version
pos += 1;
// heap_id_length = 7
buf[pos..pos + 2].copy_from_slice(&7u16.to_le_bytes());
pos += 2;
// io_filter_encoded_length = 0
buf[pos..pos + 2].copy_from_slice(&0u16.to_le_bytes());
pos += 2;
// flags = 0
buf[pos] = 0;
pos += 1;
// max_managed_object_size
buf[pos..pos + 4].copy_from_slice(&64u32.to_le_bytes());
pos += 4;
// next_huge_object_id (length_size)
pos += ls;
// btree_huge_objects_address (offset_size) - undefined
for i in 0..os {
buf[pos + i] = 0xFF;
}
pos += os;
// free_space_managed_blocks (length_size)
pos += ls;
// managed_block_free_space_manager_address (offset_size) - undefined
for i in 0..os {
buf[pos + i] = 0xFF;
}
pos += os;
// managed_space_in_heap (length_size)
pos += ls;
// allocated_managed_space_in_heap (length_size)
pos += ls;
// direct_block_allocation_iterator_offset (length_size)
pos += ls;
// managed_objects_count (length_size) = 1
buf[pos] = 1;
pos += ls;
// huge_objects_size (length_size)
pos += ls;
// huge_objects_count (length_size)
pos += ls;
// tiny_objects_size (length_size)
pos += ls;
// tiny_objects_count (length_size)
pos += ls;
// table_width = 4
buf[pos..pos + 2].copy_from_slice(&4u16.to_le_bytes());
pos += 2;
// starting_block_size (length_size)
match length_size {
4 => buf[pos..pos + 4].copy_from_slice(&(block_size as u32).to_le_bytes()),
8 => buf[pos..pos + 8].copy_from_slice(&block_size.to_le_bytes()),
_ => {}
}
pos += ls;
// max_direct_block_size (length_size) = 1024
match length_size {
4 => buf[pos..pos + 4].copy_from_slice(&1024u32.to_le_bytes()),
8 => buf[pos..pos + 8].copy_from_slice(&1024u64.to_le_bytes()),
_ => {}
}
pos += ls;
// max_heap_size (2) = 16
buf[pos..pos + 2].copy_from_slice(&max_heap_size.to_le_bytes());
pos += 2;
// starting_row_of_indirect_blocks (2) = 2
buf[pos..pos + 2].copy_from_slice(&2u16.to_le_bytes());
pos += 2;
// root_block_address (offset_size) = dblock_offset
match offset_size {
4 => buf[pos..pos + 4].copy_from_slice(&(dblock_offset as u32).to_le_bytes()),
8 => buf[pos..pos + 8].copy_from_slice(&(dblock_offset as u64).to_le_bytes()),
_ => {}
}
pos += os;
// current_rows_in_root_indirect_block (2) = 0 (root is direct)
buf[pos..pos + 2].copy_from_slice(&0u16.to_le_bytes());
pos += 2;
// checksum
let checksum = crate::checksum::jenkins_lookup3(&buf[0..pos]);
buf[pos..pos + 4].copy_from_slice(&checksum.to_le_bytes());
pos += 4;
let header_end = pos;
// Build direct block at dblock_offset
pos = dblock_offset;
buf[pos..pos + 4].copy_from_slice(b"FHDB");
pos += 4;
buf[pos] = 0; // version
pos += 1;
// heap_header_address (offset_size) = 0
pos += os;
// block_offset (block_offset_bytes) = 0
pos += block_offset_bytes;
// Data starts here - write known pattern
let data_start = pos;
// Write "Hello, World!" at offset 0 in the data area
let test_data = b"Hello, World!";
buf[data_start..data_start + test_data.len()].copy_from_slice(test_data);
(buf, header_end)
}
#[test]
fn parse_header() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
assert_eq!(hdr.heap_id_length, 7);
assert_eq!(hdr.io_filter_encoded_length, 0);
assert_eq!(hdr.max_managed_object_size, 64);
assert_eq!(hdr.table_width, 4);
assert_eq!(hdr.starting_block_size, 128);
assert_eq!(hdr.max_heap_size, 16);
assert_eq!(hdr.current_rows_in_root_indirect_block, 0);
assert_eq!(hdr.managed_objects_count, 1);
}
#[test]
fn decode_managed_id() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
// Build a managed heap ID:
// byte 0: version=0 (bits 6-7), type=0 (bits 4-5), reserved (bits 0-3)
// bytes 1-6: offset (max_heap_size=16 bits) then length (remaining bits)
// For offset=0, length=13:
// payload = offset | (length << 16) = 0 | (13 << 16) = 0x000D0000
let offset: u64 = 0;
let length: u64 = 13;
let payload = offset | (length << hdr.max_heap_size);
let mut id = vec![0u8; 7];
id[0] = 0x00; // type=0
for i in 0..6 {
id[1 + i] = ((payload >> (i * 8)) & 0xFF) as u8;
}
let (off, len) = hdr.decode_managed_id(&id).unwrap();
assert_eq!(off, 0);
assert_eq!(len, 13);
}
#[test]
fn read_managed_object_from_direct_block() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
// Build heap ID for the test data written in build_simple_heap.
// The test data "Hello, World!" is at the data area of the direct block.
// The direct block header is 5 + 8 + 2 = 15 bytes (for max_heap_size=16, ceil(16/8)=2).
// Wait, max_heap_size=16, ceil(16/8)=2. Header = sig(4)+ver(1)+addr(8)+bo(2) = 15.
// The data was placed at data_start = block_addr + 15.
// Since offset is from block start, the object is at offset 15 within the block.
let dblock_header_size = 5 + 8 + (hdr.max_heap_size as usize).div_ceil(8); // 15
let offset: u64 = dblock_header_size as u64;
let length: u64 = 13;
let payload = offset | (length << hdr.max_heap_size);
let mut id = vec![0u8; 7];
id[0] = 0x00;
for i in 0..6 {
id[1 + i] = ((payload >> (i * 8)) & 0xFF) as u8;
}
let obj = hdr.read_managed_object(&file_data, &id, 8).unwrap();
assert_eq!(&obj, b"Hello, World!");
}
#[test]
fn invalid_signature() {
let mut data = vec![0u8; 128];
data[0..4].copy_from_slice(b"XXXX");
let err = FractalHeapHeader::parse(&data, 0, 8, 8).unwrap_err();
assert_eq!(err, FormatError::InvalidFractalHeapSignature);
}
#[test]
fn invalid_version() {
let mut data = vec![0u8; 128];
data[0..4].copy_from_slice(b"FRHP");
data[4] = 1; // bad version
let err = FractalHeapHeader::parse(&data, 0, 8, 8).unwrap_err();
assert_eq!(err, FormatError::InvalidFractalHeapVersion(1));
}
#[test]
fn invalid_heap_id_type() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
// Type = 1 (huge) in bits 4-5 is not a managed ID
let id = vec![0x10u8, 0, 0, 0, 0, 0, 0];
let err = hdr.decode_managed_id(&id).unwrap_err();
assert_eq!(err, FormatError::InvalidHeapIdType(1));
}
#[test]
fn tiny_object_is_read_from_the_id() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
// Type 2 (0x20), length - 1 in the low 4 bits, data after.
let id = [0x20 | 2, b'a', b'b', b'c', 0, 0, 0];
assert_eq!(hdr.read_managed_object(&file_data, &id, 8).unwrap(), b"abc");
// A length running past the ID is an error, not a short read.
let id = [0x20 | 9, b'a', b'b', b'c', 0, 0, 0];
assert!(hdr.read_managed_object(&file_data, &id, 8).is_err());
}
#[test]
fn huge_object_with_a_direct_id() {
// With IDs long enough for an address and a length, libhdf5 stores
// huge objects' location in the ID instead of the huge-object B-tree.
let (mut file_data, _) = build_simple_heap(8, 8);
let mut hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
hdr.heap_id_length = 17;
file_data[900..905].copy_from_slice(b"huge!");
let mut id = vec![0x10u8];
id.extend_from_slice(&900u64.to_le_bytes());
id.extend_from_slice(&5u64.to_le_bytes());
assert_eq!(
hdr.read_managed_object(&file_data, &id, 8).unwrap(),
b"huge!"
);
}
#[test]
fn unknown_heap_id_version_is_refused() {
let (file_data, _) = build_simple_heap(8, 8);
let hdr = FractalHeapHeader::parse(&file_data, 0, 8, 8).unwrap();
let id = [0x40u8, 0, 0, 0, 0, 0, 0];
assert!(hdr.read_managed_object(&file_data, &id, 8).is_err());
}
/// Headers, and managed (in a direct root and through an indirect
/// root), huge and tiny objects read identically through a
/// `read_at`-only storage, for every truncation of the file.
#[test]
fn storage_reads_match_slice_reads() {
use crate::storage::CountingStorage;
let (mut file, header_end) = build_simple_heap(8, 8);
// An indirect root block at 600: row 0 holds the direct block at
// 256, then three undefined blocks.
file[600..604].copy_from_slice(b"FHIB");
let mut at = 600 + 5 + 8 + 2;
for addr in [256u64, u64::MAX, u64::MAX, u64::MAX] {
file[at..at + 8].copy_from_slice(&addr.to_le_bytes());
at += 8;
}
file[900..905].copy_from_slice(b"huge!");
let managed_id = |offset: u64, len: u64| {
let payload = offset | (len << 16);
let mut id = vec![0u8];
id.extend_from_slice(&payload.to_le_bytes()[..6]);
id
};
let mut huge = vec![0x10u8];
huge.extend_from_slice(&900u64.to_le_bytes());
huge.extend_from_slice(&5u64.to_le_bytes());
let ids = [
managed_id(15, 13),
managed_id(15, 200),
managed_id(130, 4),
huge,
vec![0x22, b'a', b'b', b'c', 0, 0, 0],
];
let mut cuts: Vec<usize> = (0..=header_end + 1).collect();
cuts.extend([256, 260, 271, 280, 600, 610, 620, 640, 900, 903, file.len()]);
for cut in cuts {
let f = &file[..cut];
let storage = CountingStorage::new(f.to_vec());
let want = FractalHeapHeader::parse(f, 0, 8, 8);
let got = FractalHeapHeader::parse_in(&storage, 0, 8, 8);
assert_eq!(format!("{got:?}"), format!("{want:?}"), "cut {cut}");
let Ok(direct) = want else { continue };
let mut indirect = direct.clone();
indirect.root_block_address = 600;
indirect.current_rows_in_root_indirect_block = 1;
let mut huge_ids = direct.clone();
huge_ids.heap_id_length = 17;
for hdr in [&direct, &indirect, &huge_ids] {
for id in &ids {
assert_eq!(
hdr.read_managed_object_in(&storage, id, 8),
hdr.read_managed_object(f, id, 8),
"cut {cut}"
);
}
}
}
}
/// A header claiming a huge doubling table (width 0xFFFF, 0xFFFF rows in
/// the root indirect block) in a 16 MiB file: reading an object from the
/// table's first block reads the entries up to it, not the rest of the
/// file, and gives what the slice read gives. When the covering entry is
/// unallocated the walk goes on over the whole block, still identically.
#[test]
fn huge_table_claims_read_only_what_the_walk_needs() {
use crate::storage::CountingStorage;
let (mut file, _) = build_simple_heap(8, 8);
file.resize(16 << 20, 0);
file[600..604].copy_from_slice(b"FHIB");
let first_entry = 600 + 5 + 8 + 2;
file[first_entry..first_entry + 8].copy_from_slice(&256u64.to_le_bytes());
let mut hdr = FractalHeapHeader::parse(&file, 0, 8, 8).unwrap();
hdr.table_width = 0xFFFF;
hdr.root_block_address = 600;
hdr.current_rows_in_root_indirect_block = 0xFFFF;
let managed_id = |offset: u64, len: u64| {
let payload = offset | (len << 16);
let mut id = vec![0u8];
id.extend_from_slice(&payload.to_le_bytes()[..6]);
id
};
let storage = CountingStorage::new(file.clone());
let id = managed_id(15, 13);
let want = hdr.read_managed_object(&file, &id, 8);
assert!(want.is_ok(), "{want:?}");
storage.reset();
assert_eq!(hdr.read_managed_object_in(&storage, &id, 8), want);
assert!(
storage.bytes_read() < 1024,
"{} bytes in {} reads",
storage.bytes_read(),
storage.reads()
);
// The second entry (heap offsets 128..256) is unallocated (zero is
// not the undefined address, so make it all ones).
file[first_entry + 8..first_entry + 16].fill(0xFF);
let storage = CountingStorage::new(file.clone());
let id = managed_id(130, 4);
let want = hdr.read_managed_object(&file, &id, 8);
assert_eq!(hdr.read_managed_object_in(&storage, &id, 8), want);
}
/// A huge object found through the huge-object B-tree reads the
/// B-tree through Storage: the same result (here an error, there is no
/// B-tree at that address) as from the slice.
#[test]
fn huge_object_btree_reads_through_storage() {
use crate::storage::CountingStorage;
let (file, _) = build_simple_heap(8, 8);
let mut hdr = FractalHeapHeader::parse(&file, 0, 8, 8).unwrap();
hdr.huge_btree_address = 700;
let id = [0x10, 1, 0, 0, 0, 0, 0];
let want = hdr.read_managed_object(&file, &id, 8);
assert!(want.is_err());
let storage = CountingStorage::new(file);
assert_eq!(hdr.read_managed_object_in(&storage, &id, 8), want);
}
/// A header with an I/O filter pipeline (read in a second, longer
/// window) parses identically through a `read_at`-only storage, for
/// every truncation.
#[test]
fn filtered_header_parses_identically_through_storage() {
use crate::storage::CountingStorage;
let (simple, header_end) = build_simple_heap(8, 8);
let pipeline = [2u8, 1, 1, 0, 0, 0, 1, 0, 6, 0, 0, 0]; // deflate, level 6
let mut header = simple[..header_end - 4].to_vec();
header[7..9].copy_from_slice(&(pipeline.len() as u16).to_le_bytes());
header.extend_from_slice(&100u64.to_le_bytes()); // root block's stored size
header.extend_from_slice(&0u32.to_le_bytes()); // its filter mask
header.extend_from_slice(&pipeline);
let sum = crate::checksum::jenkins_lookup3(&header);
header.extend_from_slice(&sum.to_le_bytes());
let mut file = header.clone();
file.resize(256, 0);
let hdr = FractalHeapHeader::parse(&file, 0, 8, 8).unwrap();
assert!(hdr.filter_pipeline.is_some());
for cut in 0..=file.len() {
let f = &file[..cut];
let storage = CountingStorage::new(f.to_vec());
assert_eq!(
format!("{:?}", FractalHeapHeader::parse_in(&storage, 0, 8, 8)),
format!("{:?}", FractalHeapHeader::parse(f, 0, 8, 8)),
"cut {cut}"
);
}
}
}